I just found this and our appologies for the delay. I assume that you have a reasonable size stone chimney. I am unsure as to what you mean as a boot as these are typically used only on round penetrations in smaller sizes.
If you are referring to flashing around a chimney, each metal system has its own methods. First I would check with the manufacturer.
Having said that rock chimneys are very difficult to flash with the uneven surface and random joints. Red rock can also tend to be porous at times and let water in up higher.
We have found that the best method is to create a raised box of 1 1/2" material around the chimney first at least 3" high depending on the location and pitch of the roof. Install your metal sheets and bent\d them up against the chimney. You can now have a counter flashing made in a "Z" shape to sit on the box and cover the sheet edge and have it go up the chimney at least 2" with an outward 1/2" kick on 45 degrees at the top.
You can now bend the upper edge to follow the rock face and fasten with plastic masonry drive pins. Finish by filling the flanged upper grouve with a high quality 2 part Butyl caulking.
Hope this is clear enough and helps out.

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